Citations in PubMed

Primary Citation PubMed: 24305160 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Intracellular long-chain acyl CoAs activate TRPV1 channels.

(2014) PLoS One 9

PubMed: 24798548 | PubMedCentral: PMC4010479 | DOI: 10.1371/journal.pone.0096597

All molecular modeling is based on the 3.4 Å resolution TRPV1 structure determined by electron cryo-microscopy (PDB# 3J5P, [37] , [38] ).

Publication Year: 2014


A structural view of ligand-dependent activation in thermoTRP channels.

(2014) Front Physiol 5

PubMed: 24847275 | PubMedCentral: PMC4017155 | DOI: 10.3389/fphys.2014.00171

Inspection of apo and ligand-bound structures of TRPV1 (Cao et al., 2013b ; Liao et al., 2013 ; PDB IDs: 3J5P, 3J5Q, and 3J5R), identified a binding pocket suitable to fit one PIP 2 molecule connectin... TM5 and TM6 from one subunit with the TM5-TM6 linker of the neighbor subunit (Figure 2A ).

TRPV1 structure (PDB ID 3J5P) was visualized and colored using PyMOL Molecular Graphics System.

In order to get a better placement of the lateral chains of the available structure, the TRPV1 channel (PDB ID 3J5P) was embedded in lipids (POPC), and placed in a periodic box containing water and ions (140 mM KCl).

Publication Year: 2014


Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

(2013) Nature 504

PubMed: 24305160 | PubMedCentral: PMC4078027 | DOI: 10.1038/nature12822

The coordinates of atomic model of TRPV1 have been deposited in the Protein Data Bank under the accession number: 3J5P.

Publication Year: 2013


TRPV channel-mediated calcium transients in nociceptor neurons are dispensable for avoidance behaviour.

(2014) Nat Commun 5

PubMed: 25178952 | PubMedCentral: PMC4164786 | DOI: 10.1038/ncomms5734

We relied on structurally resolved potassium channels Kv1.2-2.1 Paddle Chimera Channel (PDB ID: 2R9R), the chicken inward-rectifier K + channel Kir2.2 (PDB ID: 3JYC) and TRPV1 cryo-EM structures (PDB ... D: 3J5P) as templates 56 57 58 59 .

Publication Year: 2014


Dissecting domain-specific evolutionary pressure profiles of transient receptor potential vanilloid subfamily members 1 to 4.

(2014) PLoS One 9

PubMed: 25333484 | PubMedCentral: PMC4204936 | DOI: 10.1371/journal.pone.0110715

The grey shaded area indicates the tridimensional structure contacts (3J5P).

Evolutionary constraints and conservation plots To map residue and domain conservation on the specific domains, we used the ConSurf server [46] using the 3J5P TRPV1 structure as template.

Conservation degree for each amino acid position was plotted on the solved structure for TRPV1 (pdb code 3J5P) for the MSAs for TRPV1-4 and TRPV1.

For the conservation plot of TRPV2, TRPV3 and TRPV4 homology models were built based on the coordinates of TRPV1 (pdb code 3J5P).

To discriminate the residues involved in monomer-to-monomer contacts, we have mapped the subunit A (inter-chain) contacts from the PDB file (3J5P) in Fig. 4C .

Evolutionary constraints of the TRPVs TMD domain were predicted using the EVcouplings server [18] and the inter-chain crystal contacts for rat TRPV1 structure, PDB code 3J5P [17] were analyzed using the contact map analysis tool from the SPACE suite [47] .

Table S2 Inter-chain structure contacts for chain A obtained for the rat TRPV1 transmembrane domain segment high-resolution structure (PDB code 3J5P).

Publication Year: 2014


Correction: intracellular long-chain acyl CoAs activate TRPV1 channels.

(2015) PLoS One 10

PubMed: 25689159 | PubMedCentral: PMC4331288 | DOI: 10.1371/journal.pone.0118385

All molecular modeling is based on the 3.4 Å resolution TRPV1 structure determined by electron cryo-microscopy (PDB# 3J5P,[37],[38]).

Publication Year: 2015


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4338550

PDB accession codes: 2R9R for the Kv1.2/Kv2.1 paddle chimera, 4DXW for Na v Rh, and 3J5P for TRPV1.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4530436

(B) Top-ranked (according to MODELLER score) mouse TRPC3 homology model on the TRPV1 apo structure (PDB entry 3J5P) with the Kv 1.2/2.1 channel chimera structure for the S4–S5 linker shown fro... a top view and a side view.

(C) Structure of apo TRPV1 (PDB entry 3J5P) with mutants in the S4–S5 linker region found to have significant effects on TRP channel function highlighted with red dots.

In total, five templates were used in homology modeling: the Kv 1.2/2.1 chimera structure (PDB entry 2R9R), the TRPV1 apo structure (PDB entry 3J5P), the TRPV1 apo structure (PDB entry 3J5P) with the Kv 1.2/2.1 channel chimera structure for the S4–S5 linker, the TRPV1 DkTx- and RTX-bound structure (PDB entry 3J5Q) with the Kv 1.2/2.1 channel chimera structure for the S4–S5 linker, and the TRPV1 capsaicin-bound structure (PDB entry 3J5R) with the Kv 1.2/2.1 channel chimera structure for the S4–S5 linker.

Publication Year: 2015